# load libraries
library(here)
library(ggpmisc)
library(ggrepel)
library(ggbeeswarm)
library(cowplot)
library(knitr)
library(ggcorrplot)
library(ggpubr)
library(ggbiplot)
library(tidyverse) # load this last to minimize conflictsImport the data
# Read the data
tl <- read_csv(here::here("data/raw-data/Tulai_Lithic_Assamblage.csv"))
# this file is prepared from the google sheet here
# https://docs.google.com/spreadsheets/d/1Q0QZESk412ZQLE24yPs6Rg-7Y9OMX63DHoXeIPNAIFM/edit#gid=0
# and simplified using code in the scraps.R file
excavation_data <-
read_csv(here::here("data//raw-data/excavation_data.csv"))Clean the data
# Create a new data frame with renamed columns
tl1 <- tl
names(tl1)[1:2] <- c("lithic_id",
"TA")
# modify TA column
tl1 <- tl1 %>%
# Remove everything within brackets
mutate(TA = str_remove_all(TA,
"\\(.*\\)")) %>%
# Add slash between TA and numbers
mutate(TA = str_replace_all(TA,
"TA([0-9]+)",
"TA/\\1")) %>%
# Add slash between numbers
mutate(TA = str_replace_all(TA,
"([0-9]+)/([0-9]+)", "\\1/\\2")) %>%
# fill NA values in TA column
tidyr::fill(TA, .direction = "down") %>%
# Prepend 'TA/' to numbers
mutate(TA = if_else(str_detect(TA,
"^[0-9]+$"),
paste0("TA/",
TA),
TA)) %>%
# Remove all non-alphanumeric characters
mutate(TA = str_replace_all(TA,
"[^[:alnum:] /]",
"")) %>%
# Make all text lowercase
mutate(TA = tolower(TA)) %>%
# Remove white space
mutate(TA = str_replace_all(TA, " ", "")) %>%
# Separate 'TA' column into 'area' and 'depth' columns
separate(TA, into = c("area",
"depth"),
sep = "/",
remove = FALSE,
convert = TRUE) %>%
# Convert 'depth' to numeric
mutate(depth = as.numeric(depth)) %>%
# Create depth ranges
mutate(depth = case_when(
depth == 3 ~ "0-30 cm",
depth == 34 ~ "30-40 cm",
depth == 45 ~ "40-50 cm",
depth == 56 ~ "50-60 cm",
depth == 67 ~ "60-70 cm",
depth == 72 ~ "70-120 cm",
depth == 125 ~ "120-150 cm",
depth == 158 ~ "150-180 cm",
depth == 189 ~ "180-190 cm",
depth == 190 ~ "190-200 cm",
depth == 201 ~ "200-210 cm",
depth == 212 ~ "210-220 cm",
depth == 223 ~ "220-230 cm",
depth == 234 ~ "230-240 cm",
depth == 235 ~ "230-250 cm",
depth == 256 ~ "250-260 cm",
depth == 267 ~ "260-270 cm",
depth == 72 ~ "70-120 cm",
depth == 1 ~ "0-10 cm",
depth == 2 ~ "0-20 cm",
depth == 13 ~ "10-30 cm",
depth == 19 ~ "10-90 cm",
depth == 23 ~ "20-30 cm",
depth == 34 ~ "30-40 cm",
depth == 45 ~ "40-50 cm",
depth == 51 ~ "50-100 cm",
depth == 56 ~ "50-60 cm",
depth == 57 ~ "50-70 cm",
depth == 89 ~ "80-90 cm",
depth == 91 ~ "90-100 cm",
depth == 101 ~ "100-110 cm",
depth == 112 ~ "110-120 cm",
depth == 123 ~ "120-130 cm",
depth == 124 ~ "120-140 cm",
depth == 23 ~ "20-30 cm",
depth == 46 ~ "40-60 cm",
depth == 78 ~ "70-80 cm",
depth == 235 ~ "230-250 cm",
depth == 12 ~ "10-20 cm",
depth == 90 ~ "90-100 cm",
TRUE ~ as.character(depth)
)) %>%
separate(depth,
into = c("upper",
"lower"),
sep = "-",
remove = FALSE,
convert = TRUE) %>%
mutate(lower = parse_number(lower)) %>%
rowwise() %>%
mutate(midpoint = mean(c(upper, lower))) %>%
# create 'chronological unit' column
mutate(chronological_unit = case_when(
area == "tp1" & depth == "0-10 cm" ~ "c",
area == "tp1" & depth == "0-20 cm" ~ "c",
area == "tp1" & depth == "10-30 cm" ~ "c",
area == "tp1" & depth == "10-90 cm" ~ "c",
area == "tp1" & depth == "20-30 cm" ~ "c",
area == "tp1" & depth == "30-40 cm" ~ "c",
area == "tp1" & depth == "40-50 cm" ~ "c",
area == "tp1" & depth == "50-100 cm" ~ "c",
area == "tp1" & depth == "50-60 cm" ~ "b",
area == "tp1" & depth == "50-70 cm" ~ "b",
area == "tp1" & depth == "80-90 cm" ~ "b",
area == "tp1" & depth == "90-100 cm" ~ "b",
area == "tp1" & depth == "100-110 cm" ~ "b",
area == "tp1" & depth == "110-120 cm" ~ "b",
area == "tp1" & depth == "120-130 cm" ~ "b",
area == "tp1" & depth == "120-140 cm" ~ "b",
area == "d1" & depth == "0-20 cm" ~ "c",
area == "d1" & depth == "20-30 cm" ~ "c",
area == "d1" & depth == "40-60 cm" ~ "a",
area == "d1" & depth == "50-60 cm" ~ "a",
area == "d1" & depth == "60-70 cm" ~ "a",
area == "d1" & depth == "70-80 cm" ~ "a",
area == "ta" & depth == "0-30 cm" ~ "e",
area == "ta" & depth == "30-40 cm" ~ "e",
area == "ta" & depth == "40-50 cm" ~ "e",
area == "ta" & depth == "50-60 cm" ~ "e",
area == "ta" & depth == "60-70 cm" ~ "e",
area == "ta" & depth == "70-120 cm" ~ "d",
area == "ta" & depth == "120-150 cm" ~ "d",
area == "ta" & depth == "150-180 cm" ~ "d",
area == "ta" & depth == "180-190 cm" ~ "d",
area == "ta" & depth == "190-200 cm" ~ "d",
area == "ta" & depth == "200-210 cm" ~ "d",
area == "ta" & depth == "210-220 cm" ~ "d",
area == "ta" & depth == "220-230 cm" ~ "d",
area == "ta" & depth == "230-240 cm" ~ "d",
area == "ta" & depth == "230-250 cm" ~ "d",
area == "ta" & depth == "250-260 cm" ~ "d",
area == "ta" & depth == "260-270 cm" ~ "d",
TRUE ~ NA_character_
)) %>%
mutate(
grouped_level = case_when(
area == "tp1" & depth == "0-10 cm" ~ "3",
area == "tp1" & depth == "0-20 cm" ~ "3",
area == "tp1" & depth == "10-30 cm" ~ "3",
area == "tp1" & depth == "10-90 cm" ~ "3",
area == "tp1" & depth == "20-30 cm" ~ "3",
area == "tp1" & depth == "30-40 cm" ~ "3",
area == "tp1" & depth == "40-50 cm" ~ "3",
area == "tp1" & depth == "50-100 cm" ~ "3",
area == "tp1" & depth == "50-60 cm" ~ "2",
area == "tp1" & depth == "50-70 cm" ~ "2",
area == "tp1" & depth == "80-90 cm" ~ "2",
area == "tp1" & depth == "90-100 cm" ~ "2",
area == "tp1" & depth == "100-110 cm" ~ "1",
area == "tp1" & depth == "110-120 cm" ~ "1",
area == "tp1" & depth == "120-130 cm" ~ "1",
area == "tp1" & depth == "120-140 cm" ~ "1",
area == "d1" & depth == "0-20 cm" ~ "3",
area == "d1" & depth == "20-30 cm" ~ "3",
area == "d1" & depth == "40-60 cm" ~ "2",
area == "d1" & depth == "50-60 cm" ~ "2",
area == "d1" & depth == "60-70 cm" ~ "1",
area == "d1" & depth == "70-80 cm" ~ "1",
area == "ta" & depth == "0-30 cm" ~ "6",
area == "ta" & depth == "30-40 cm" ~ "6",
area == "ta" & depth == "40-50 cm" ~ "5",
area == "ta" & depth == "50-60 cm" ~ "5",
area == "ta" & depth == "60-70 cm" ~ "5",
area == "ta" & depth == "70-120 cm" ~ "4",
area == "ta" & depth == "120-150 cm" ~ "4",
area == "ta" & depth == "150-180 cm" ~ "3",
area == "ta" & depth == "180-190 cm" ~ "3",
area == "ta" & depth == "190-200 cm" ~ "2",
area == "ta" & depth == "200-210 cm" ~ "2",
area == "ta" & depth == "210-220 cm" ~ "2",
area == "ta" & depth == "220-230 cm" ~ "2",
area == "ta" & depth == "230-240 cm" ~ "2",
area == "ta" & depth == "230-250 cm" ~ "1",
area == "ta" & depth == "250-260 cm" ~ "1",
area == "ta" & depth == "260-270 cm" ~ "1",
TRUE ~ NA_character_
)
)
# Remove specific columns
tl1 %>%
select(-c("AREA",
"DEPTH (cm)",
"Raw Material",
"Colour/Grain/Opacity",
"Pattern"))# A tibble: 3,920 × 37
# Rowwise:
lithic_id TA area depth upper lower `Cortex (%)` `Weight (g)`
<chr> <chr> <chr> <chr> <int> <dbl> <dbl> <lgl>
1 1 ta/34 ta 30-40 cm 30 40 0 NA
2 2 ta/34 ta 30-40 cm 30 40 0 NA
3 3 ta/34 ta 30-40 cm 30 40 0 NA
4 4 ta/34 ta 30-40 cm 30 40 0 NA
5 5 ta/34 ta 30-40 cm 30 40 0 NA
6 6 ta/34 ta 30-40 cm 30 40 0 NA
7 9 ta/34 ta 30-40 cm 30 40 0 NA
8 10 ta/34 ta 30-40 cm 30 40 0 NA
9 11 ta/34 ta 30-40 cm 30 40 10 NA
10 12 ta/34 ta 30-40 cm 30 40 0 NA
# ℹ 3,910 more rows
# ℹ 29 more variables: `Length (mm)` <dbl>, `Width (mm)` <dbl>,
# `Thickness (mm)` <chr>, `Bulb Thickness (mm)` <chr>,
# `Platform Thickness (mm)` <chr>, `platform Length (mm)` <chr>,
# Eraillure <chr>, Typology <chr>, Utilization <chr>, Retouch <dbl>,
# `Retouch Position` <chr>, `Retouch Localization` <chr>,
# `Retouch Distribution` <chr>, `Retouch Intensity` <chr>, …# exploring Data
p1 <-
tl1 %>%
group_by(midpoint) %>%
tally() %>%
drop_na(midpoint) %>%
ggplot() +
aes(midpoint, n) +
geom_col()
p2 <-
tl1 %>%
group_by(chronological_unit) %>%
tally() %>%
drop_na(chronological_unit) %>%
ggplot() +
aes(chronological_unit, n) +
geom_col()
plot_grid(p1, p2, ncol = 1)
# exploring Data
tl2 <- tl1 %>%
mutate(
Blank = case_when(
Breakage %in% c("0", "1", NA_character_) ~ Blank,
TRUE ~ Breakage
)
)# Cleaning Blank column
tl2 <- tl2 %>%
mutate(
Blank = str_to_lower(Blank),
Blank = str_trim(Blank),
Blank = str_replace_all(Blank, "[./]", "-"),
Blank = str_replace_all(Blank, "\\s*-\\s*", "-")
) %>%
mutate(Blank = case_when(
Blank == "peo" ~ "bladelet-pro",
Blank == "pro" ~ "bladelet-pro",
Blank == "bladelet-dis" ~ "bladelet-dis",
Blank == "microblade" ~ "bladelet-complete",
Blank == "microblade-pro" ~ "bladelet-pro",
Blank == "microblade-med" ~ "bladelet-med",
Blank == "micrpblade-dis" ~ "bladelet-dis",
Blank == "dis" ~ "bladelet-dis",
Blank == "bladelrt-med" ~ "bladelet-med",
Blank == "bladelet-mes" ~ "bladelet-med",
Blank == "bladelet-,ed" ~ "bladelet-med",
Blank == "bladelet-bladelet-med" ~ "bladelet-med",
Blank == "medial" ~ "bladelet-med",
Blank == "bladelet-bladelet-pro" ~ "bladelet-pro",
Blank == "bladelert-pro" ~ "bladelet-pro",
Blank == "microblade-medial" ~ "bladelet-med",
Blank == "nicroblade-pro" ~ "bladelet-pro",
Blank == "microblade-?" ~ "bladelet-complete",
Blank == "med" ~ "bladelet-med",
Blank == "bladeler-pro" ~ "bladelet-pro",
Blank == "microblade-dis" ~ "bladelet-dis",
Blank == "microblde-dis" ~ "bladelet-dis",
Blank == "bladlet-pro" ~ "bladelet-pro",
Blank == "indistinct" ~ "bladelet-med",
Blank == "flake" ~ "flake-complete",
Blank == "dladelet-pro" ~ "bladelet-pro",
Blank == "dladelet-pro" ~ "bladelet-pro",
Blank == "bldelet-bladelet-pro" ~ "bladelet-pro",
Blank == "bldelet-pro" ~ "bladelet-pro",
Blank == "nicroblade-pro" ~ "bladelet-pro",
Blank == "microblade-?" ~ "bladelet-med",
Blank == "bladelt-pro" ~ "bladelet-pro",
Blank == "bladeket-med" ~ "bladelet-med",
Blank == "nicroblade-pro" ~ "bladelet-pro",
Blank == "blaelet" ~ "bladelet-complete",
Blank == "bladele-med" ~ "bladelet-med",
Blank == "bladelet-nearly complete" ~ "bladelet-complete",
Blank == "blade-nearly complete" ~ "blade-complete",
Blank == "bladelet-?" ~ "bladelet-complete",
Blank == "flake?" ~ "flake-complete",
Blank == "micrpblade-dis" ~ "bladelet-dis",
Blank == "blaelet-med" ~ "bladelet-med",
Blank == "blaedlet-pro" ~ "bladelet-pro",
Blank == "bladelt-pro" ~ "bladelet-pro",
Blank == "bladelet-nearly complete"~ "bladelet-complete",
Blank == "microblade-med" ~ "bladelet-med",
Blank == "bldelet-bladelet-pro" ~ "bladelet-pro",
Blank == "bldelet-flake" ~ "blade-complete",
Blank == "mwdial" ~ "bladelet-med",
Blank == "blade" ~ "blade-complete",
Blank == "bladelt" ~ "bladelet-complete",
Blank == "bladlet" ~ "bladelet-complete",
Blank == "bladlet-med" ~ "bladelet-med",
Blank == "bladelt-med" ~ "bladelet-med",
Blank == "flaje" ~ "flake",
Blank == "flke" ~ "flake",
Blank == "bladelet" ~ "bladelet-complete",
Blank == "NA" ~ "bladelet-",
Blank == "thick flake" ~ "flake",
Blank == "flke-mid" ~ "flake-med",
Blank == "flake-blade" ~ "flake",
Blank == "angular flake?" ~ "flake",
Blank == "flake-prox" ~ "flake-pro",
Blank == "fklae-dis" ~ "flake-dis",
Blank == "bladelete" ~ "bladelet",
Blank == "NA" ~ NA_character_,
TRUE ~ Blank
)) %>%
mutate(Blank = na_if(Blank, ""))
# rev(sort(table(tl2$Blank)))
# BM: still many typos and unusual categories in here, why is that? Can they be fixed? This might increase our sample size.
tl3 <- tl2 %>%
separate(Blank,
into = c("Blank2", "Blank_part"),
sep = "-",
remove = FALSE,
convert = TRUE)
na_rows <- which(is.na(tl2$Blank))
zero_rows <- which(tl2$Blank == "0")
one_rows <- which(tl2$Blank == "1")
# rev(sort(table(tl3$Blank2))) # BM: this is an unusual coding pattern, I'm curious about where you got it from?
tl3 <- tl3 %>%
mutate(
Blank2 = case_when(
Blank2 == "flake" ~ "flake", # Keep "flake" as it is
(`Core Typology` %in% c("0", "NA", "na", "-", ".") |
is.na(`Core Typology`) |
`Core Typology` == "") & `Width (mm)` < 12 ~ "bladelet",
(`Core Typology` %in% c("0", "NA", "na", "-", ".") |
is.na(`Core Typology`) |
`Core Typology` == "") & `Width (mm)` >= 12 ~ "blade",
TRUE ~ Blank2
)
) %>%
mutate(
Blank2 = case_when(
Blank2 %in% c("blade", "bladelet", "flake") ~ Blank2,
TRUE ~ NA_character_
)
)# SS: they are natural rocks, and don't want to count them as lithic
# BM: better to remove them by their ID than by row number, since row number can easily change, but ID cannot
tl3 <- tl3 %>%
filter(!lithic_id %in% c("3154", "1741", "1680", "طبیعی"))tl4 <- tl3 %>%
mutate(
Utilization = if_else(Retouch == "1",
NA_character_,
as.character(Utilization))
)tl4 <- tl4 %>%
# BM: I updated this to use across
mutate(across(everything(),
~ifelse(is.na(.x)|.x == ""|.x == "-", NA, .x))) %>%
#SS: remove any asterisks, whitespace, or *, ?, or !. is that wrong?
mutate(across(everything(),
~str_replace(., "(?<=\\D)\\*(?=\\D)|\\s+|[*?!]+", ""))) %>%
##SS: we meant sickle shine, this is one of the criteria based on which Hole claimed the site is not related to agriculture (similar to ALi Kosh located in Dehluran)
mutate(
SHINE = str_trim(SHINE) %>%
str_to_title(),
shine2 = SHINE
) %>%
mutate(
shine2 = case_when(
SHINE %in% c("Subparallel",
"Parallel",
"Sub-Parallel",
"Parallel-Subprarallel",
"Scaled",
"Sub-Paralel",
"Sub-Parallell",
"Sub-Paallel",
"Sub-Paralell",
"Sub-Prallel",
"L:semiparallel/R:scaled",
"L:semiparallel/R: Scaled",
"Semiparallel",
"Semi-Parallel",
"Scaled/Sub-Parallel",
"Seb-Parallel",
"Semi-Abrupt") ~ NA_character_,
TRUE ~ SHINE
),
Utilization = if_else(Utilization == "0", NA, Utilization),
Retouch = if_else(Retouch == "0", NA, Retouch),
SHINE = if_else(SHINE == "0", NA, SHINE),
shine2 = if_else(shine2 == "0", NA, shine2),
Blank2 = if_else(Blank2 == "0", NA, Blank2)
) %>%
mutate(
SHINE = na_if(SHINE, "")
)
# BM: I think this is a better way to inspect:
# rev(sort(table(tl4$SHINE)))
# rev(sort(table(tl4$shine2)))tl4 <- tl4 %>%
mutate(
`Core Typology` = str_to_lower(`Core Typology`),
`Core Typology` = str_trim(`Core Typology`),
# BM: what does this regex do in the next line?
`Core Typology` = str_replace_all(`Core Typology`, "^[-._/NA\\s]*$|^\\s*$", "0")
) %>%
mutate(`Core Typology` = case_when(
`Core Typology` == "flatcore" ~ "flat-pressure",
`Core Typology` == "rejuvention" ~ "rejuvenation piece-NA",
`Core Typology` == "pressureprymidal core" ~ "pyramid-pressure",
`Core Typology` == "pressureflat core" ~ "flat-pressure",
`Core Typology` == "pressurebullet core" ~ "bullet-pressure",
`Core Typology` == "prussurebullet core" ~ "bullet-pressure",
`Core Typology` == "prismaticcore" ~ "cylinder/prismatic-percussion",
`Core Typology` == "pyramidalpressure core" ~ "pyramid-pressure",
`Core Typology` == "flatcore with one debitage surface/pressure" ~ "flat-pressure",
`Core Typology` == "corefragment" ~ "core fragment-NA",
`Core Typology` == "cilandrical/pressure" ~ "cylinder/prismatic-pressure",
`Core Typology` == "bullet/pressure" ~ "bullet-pressure",
`Core Typology` == "pyramidal/pressure" ~ "pyramid-pressure",
`Core Typology` == "percussion/pyramidal" ~ "pyramid-pressure",
`Core Typology` == "flat/pressure" ~ "flat-pressure",
`Core Typology` == "pyramidal/ percussion??" ~ "pyramid-pressure",
`Core Typology` == "pyramidal/ peressure" ~ "pyramid-pressure",
`Core Typology` == "pyramidal/ pressure" ~ "pyramid-pressure",
`Core Typology` == "pressure" ~ "pyramid-pressure",
`Core Typology` == "multidirectional/percussion" ~ "shapeless-percussion",
`Core Typology` == "prismatic/ percussion" ~ "pyramid-pressure",
`Core Typology` == "flatcore/ unidirectional/pressure" ~ "flat-pressure",
`Core Typology` == "heavilyused" ~ "NA",
`Core Typology` == "burnt" ~ "NA",
`Core Typology` == "patinated" ~ "NA",
`Core Typology` == "pyramidal(bullet)/pressure" ~ "bullet-pressure",
`Core Typology` == "cylandrycal/ bidirectional pressure core" ~ "bullet-pressure",
`Core Typology` == "pyramidal/unidirectional pressure bullet core" ~ "bullet-pressure",
`Core Typology` == "pyramidal/unidirectional pressure core" ~ "pyramid-pressure",
`Core Typology` == "pyramidal/unidirectional pressure core" ~ "pyramid-pressure",
`Core Typology` == "bladelet" ~ "bullet-pressure",
`Core Typology` == "lip" ~ "NA",
`Core Typology` == "bladlet" ~ "bullet-pressure",
`Core Typology` == "bladelet(30.56)" ~ "pyramid-pressure",
`Core Typology` == "bladelet(28.55.6)" ~ "bullet-pressure",
`Core Typology` == "bladelet(16.28.1)" ~ "bullet-pressure",
`Core Typology` == "bladelet(40 5.7)" ~ "pyramid-pressure",
`Core Typology` == "bladelet(23.2 2.3)" ~ "bullet-pressure",
`Core Typology` == "bladelet-flakeblade(41 16)" ~ "bullet-pressure",
`Core Typology` == "bladelet(28 6.7)" ~ "bullet-pressure",
`Core Typology` == "bladelet(28 6.7)" ~ "bullet-pressure",
`Core Typology` == "bladelet(3512.6/7)" ~ "pyramid-pressure",
`Core Typology` == "bladelet(27.307.5)" ~ "bullet-pressure",
`Core Typology` == "pressure/pyramidal" ~ "pyramid-pressure",
`Core Typology` == "bladeletcore" ~ "bullet-pressure",
`Core Typology` == "pyramidal? / pressure" ~ "pyramid-pressure",
`Core Typology` == "prismatic" ~ "pyramid-pressure",
`Core Typology` == "0" ~ "",
`Core Typology` == "na" ~ "",
`Core Typology` == "na" ~ "",
TRUE ~ `Core Typology`
)) %>%
# Separate 'Core Typology' into 'core-typology' and 'core-technology'
separate(`Core Typology`,
into = c("core-typology", "core-technology"),
sep = "-",
remove = FALSE,
convert = TRUE)
# Check the unique values again
# rev(sort(table((tl4$`core-typology`))))
# rev(sort(table((tl4$`core-technology`))))tl4 <- tl4 %>%
mutate(
Typology = str_to_lower(Typology),
Typology = str_trim(Typology),
Typology = str_replace_all(Typology, "^[-._/NA\\s]*$|^\\s*$", "0")
) %>%
mutate(
# BM: wow, seems like almost each artefact is its own type!
# BM: That is not ideal for statistical analysis
# BM: This looks like it was very time-consuming to simplify.
##SS: this column was so messy with too many mistakes; I needed to have all typos correct then transfer them in their corresponding columns.
Typology = case_when(
`Typology` == "notch, truncated" ~ "tool/notch;truncated piece",
`Typology` == "retouchpiece" ~ "tool/retouched piece",
`Typology` == "endscraper" ~ "tool/end scraper",
`Typology` == "notch" ~ "tool/notch",
`Typology` == "sidescraper" ~ "tool/side scraper",
`Typology` == "doubleside scraper" ~ "tool/double side scraper",
`Typology` == "convergentscraper (?)" ~ "tool/convergent scraper",
`Typology` == "doublenotch on retouched piece" ~ "tool/double notch",
`Typology` == "retouchpieces" ~ "tool/retouched piece",
`Typology` == "burin(?)/ notch/scraper" ~ "tool/burin-notch-scraper",
`Typology` == "borer" ~ "tool/perforator-borer",
`Typology` == "retouchedpiece" ~ "tool/retouched piece",
`Typology` == "notch/side scraper" ~ "tool/notch-side scraper",
`Typology` == "corefragment" ~ "core/core fragment",
`Typology` == "backed" ~ "tool/backed knife",
`Typology` == "doubleside scraper ?" ~ "tool/double side scraper",
`Typology` == "inversedenticulate" ~ "tool/denticulate",
`Typology` == "retouchpieces/ side scraper?" ~ "tool/side scraper",
`Typology` == "sidescraper ?" ~ "tool/side scraper",
`Typology` == "notch-denticulate" ~ "tool/notch-denticulate",
`Typology` == "borer/drill" ~ "tool/perforator-drill",
`Typology` == "retouchedpiece (side scraper?)" ~ "tool/side scraper",
`Typology` == "retouchepiece (side scraper?)" ~ "tool/side scraper",
`Typology` == "retouchedpiece (double side scraper)" ~ "tool/double side scraper",
`Typology` == "retouchedpiece (double side scraper?)" ~ "tool/double side scraper",
`Typology` == "retouchepiece" ~ "tool/retouched piece",
`Typology` == "inversenotch" ~ "tool/notch",
`Typology` == "retouchepiece (double side scaraper?)" ~ "tool/double side scraper",
`Typology` == "retouchedpiece( double side scraper?)" ~ "tool/double side scraper",
`Typology` == "notchon retouche piece" ~ "tool/notch",
`Typology` == "retouchedpiece (souble side scraper)" ~ "tool/double side scraper",
`Typology` == "point" ~ "tool/perforator-point",
`Typology` == "chunk" ~ "NA/NA",
`Typology` == "coretablet" ~ "core/core tablet",
`Typology` == "core" ~ "core/shapeless",
`Typology` == "denticulate" ~ "tool/denticulate",
`Typology` == "doublenotch (haft)" ~ "tool/double notch",
`Typology` == "retouchedpiece (fine retouch)" ~ "tool/retouched piece",
`Typology` == "endscraper on retouched piece" ~ "tool/end scraper",
`Typology` == "retouchedpiece (serrated scraper)" ~ "tool/serrated scraper",
`Typology` == "truncation" ~ "tool/truncated piece",
`Typology` == "rejuventionpiece" ~ "core/rejuvenation piece",
`Typology` == "notch/denticulate" ~ "tool/notch-denticulate",
`Typology` == "retoucheduse on breakage" ~ "tool/retouched piece",
`Typology` == "inversenotch/endscraper" ~ "tool/notch-end scraper",
`Typology` == "alternatingside scraper" ~ "tool/side scraper",
`Typology` == "alternatedouble side scraper" ~ "tool/double side scraper",
`Typology` == "truncation/sidescaraper" ~ "tool/truncated piece",
`Typology` == "doublenotch" ~ "tool/double notch",
`Typology` == "borer/awl" ~ "tool/perforator-awl",
`Typology` == "roundscraper?" ~ "tool/round scraper",
`Typology` == "doublenotch scraper" ~ "tool/double notch scraper",
`Typology` == "corerejuvention (core tablet?)" ~ "core/core tablet",
`Typology` == "truncationاریبب" ~ "tool/truncated piece",
`Typology` == "retouchedpiece (side scraper)" ~ "tool/side scraper",
`Typology` == "retochedpice" ~ "tool/retouched piece",
`Typology` == "truncation/notch" ~ "tool/truncated piece-notch",
`Typology` == "doublealternate scraper" ~ "tool/double side scraper",
`Typology` == "awl/ inverse notch" ~ "tool/notch",
`Typology` == "retouchedpiece (alternate scraper?)" ~ "tool/double side scraper",
`Typology` == "inverseside scraper" ~ "tool/side scraper",
`Typology` == "usedcore rejuvention" ~ "core/rejuvenation piece",
`Typology` == "coreside rejuvention" ~ "core/rejuvenation piece",
`Typology` == "coreplatform rejuvention flake" ~ "core/rejuvenation piece",
`Typology` == "corerejuvention platform" ~ "core/rejuvenation piece",
`Typology` == "coreside rejuvention blade" ~ "core/rejuvenation piece",
`Typology` == "coreside rejuvention blade??" ~ "core/rejuvenation piece",
`Typology` == "coreedge rejuvention" ~ "core/rejuvenation piece",
`Typology` == "coreedge rejivention" ~ "core/rejuvenation piece",
`Typology` == "retouchedpice (side scraper?)" ~ "tool/side scraper" ,
`Typology` == "scraper" ~ "tool/side scraper",
`Typology` == "sickleblade" ~ "tool/sickle shine",
`Typology` == "coretool (scraper)" ~ "tool/scraper-on core piece",
`Typology` == "retouchedpiece (scraper)" ~ "tool/side scraper",
`Typology` == "inversedenticulate?" ~ "tool/denticulate",
`Typology` == "retouchedpiece (scraper?)" ~ "tool/side scraper",
`Typology` == "coreside rejuvention flake" ~ "core/rejuvenation piece",
`Typology` == "truncation/endscraper" ~ "tool/endscraper on truncated piece",
`Typology` == "retouchedpice(double side scraper?)" ~ "tool/double side scraper",
`Typology` == "doublescraper" ~ "tool/double side scraper",
`Typology` == "dendiculate" ~ "tool/denticulate",
`Typology` == "double-scraper" ~ "tool/double side scraper",
`Typology` == "pyramidalcore" ~ "core/pyramid",
`Typology` == "bulletcore" ~ "core/bullet",
`Typology` == "corerejuvention" ~ "core/rejuvenation piece",
`Typology` == "pyrmidalcore" ~ "core/pyramid",
`Typology` == "corepreperation" ~ "core/core preparation piece",
`Typology` == "crested" ~ "core/crested bladelet",
`Typology` == "preperationblade" ~ "core/core preperation",
`Typology` == "burin" ~ "tool/burin",
`Typology` == "serrateddenticulate" ~ "tool/serrated scraper",
`Typology` == "saw:serrated denticulate" ~ "tool/serrated scraper",
`Typology` == "serratedused" ~ "tool/serrated scraper",
`Typology` == "corepreeration" ~ "tool/core preparation piece",
`Typology` == "coreprepearation" ~ "tool/core preparation piece",
`Typology` == "awl" ~ "tool/perforator-awl",
`Typology` == "notch.inverse" ~ "tool/notch",
`Typology` == "point.notch" ~ "tool/perforator-point;notch",
`Typology` == "inversescraper" ~ "tool/side scraper",
`Typology` == "roundendscraper" ~ "tool/round scraper",
`Typology` == "alternate.scraper" ~ "tool/double side scraper",
`Typology` == "convergentscraper/disc scraper" ~ "tool/scraper-convergent scraper",
`Typology` == "serratedside scraper" ~ "tool/serrated scraper",
`Typology` == "debri" ~ "NA/NA",
`Typology` == "distalpart of a drill" ~ "tool/perforator-drill",
`Typology` == "corepreperation?" ~ "core/core preparation piece",
`Typology` == "preformend of a borer" ~ "tool/perforator-borer; preform",
`Typology` == "used" ~ "tool/used",
`Typology` == "distalend of a inverse sidescraper" ~ "tool/side scraper",
`Typology` == "retouchedblade" ~ "tool/retouched piece",
`Typology` == "drill" ~ "tool/perforator-drill",
`Typology` == "corerejuvention tablet" ~ "core/core tablet",
`Typology` == "bladeletcore" ~ "core/pyramid",
`Typology` == "flake-bladecore" ~ "core/mixed",
`Typology` == "notch, truncated" ~ "tool/notch;truncated piece",
`Typology` == "retouchpiece" ~ "tool/retouched piece",
`Typology` == "endscraper" ~ "tool/end scraper",
`Typology` == "notch" ~ "tool/notch",
`Typology` == "sidescraper" ~ "tool/side scraper",
`Typology` == "doubleside scraper" ~ "tool/double side scraper",
`Typology` == "convergentscraper (?)" ~ "tool/convergent scraper",
`Typology` == "doublenotch on retouched piece" ~ "tool/double notch",
`Typology` == "retouchpieces" ~ "tool/retouched piece",
`Typology` == "burin(?)/ notch/scraper" ~ "tool/burin-notch-scraper",
`Typology` == "borer" ~ "tool/perforator-borer",
`Typology` == "retouchedpiece" ~ "tool/retouched piece",
`Typology` == "notch/side scraper" ~ "tool/notch-side scraper",
`Typology` == "corefragment" ~ "core/core fragment",
`Typology` == "backed" ~ "tool/backed knife",
`Typology` == "doubleside scraper ?" ~ "tool/double side scraper",
`Typology` == "inversedenticulate" ~ "tool/denticulate",
`Typology` == "retouchpieces/ side scraper?" ~ "tool/side scraper",
`Typology` == "sidescraper ?" ~ "tool/side scraper",
`Typology` == "notch-denticulate" ~ "tool/notch-denticulate",
`Typology` == "borer/drill" ~ "tool/perforator-drill",
`Typology` == "retouchedpiece (side scraper?)" ~ "tool/side scraper",
`Typology` == "retouchepiece (side scraper?)" ~ "tool/side scraper",
`Typology` == "retouchedpiece (double side scraper)" ~ "tool/double side scraper",
`Typology` == "retouchedpiece (double side scraper?)" ~ "tool/double side scraper",
`Typology` == "retouchepiece" ~ "tool/retouched piece",
`Typology` == "inversenotch" ~ "tool/notch",
`Typology` == "retouchepiece (double side scaraper?)" ~ "tool/double side scraper",
`Typology` == "retouchedpiece( double side scraper?)" ~ "tool/double side scraper",
`Typology` == "notchon retouche piece" ~ "tool/notch",
`Typology` == "retouchedpiece (souble side scraper)" ~ "tool/double side scraper",
`Typology` == "point" ~ "tool/perforator-point",
`Typology` == "chunk" ~ "NA/NA",
`Typology` == "coretablet" ~ "core/core tablet",
`Typology` == "core" ~ "core/shapeless",
`Typology` == "denticulate" ~ "tool/denticulate",
`Typology` == "doublenotch (haft)" ~ "tool/double notch",
`Typology` == "retouchedpiece (fine retouch)" ~ "tool/retouched piece",
`Typology` == "endscraper on retouched piece" ~ "tool/end scraper",
`Typology` == "retouchedpiece (serrated scraper)" ~ "tool/serrated scraper",
`Typology` == "truncation" ~ "tool/truncated piece",
`Typology` == "rejuventionpiece" ~ "core/rejuvenation piece",
`Typology` == "notch/denticulate" ~ "tool/notch-denticulate",
`Typology` == "retoucheduse on breakage" ~ "tool/retouched piece",
`Typology` == "inversenotch/endscraper" ~ "tool/notch-end scraper",
`Typology` == "alternatingside scraper" ~ "tool/side scraper",
`Typology` == "alternatedouble side scraper" ~ "tool/double side scraper",
`Typology` == "truncation/sidescaraper" ~ "tool/truncated piece",
`Typology` == "doublenotch" ~ "tool/double notch",
`Typology` == "borer/awl" ~ "tool/perforator-awl",
`Typology` == "roundscraper?" ~ "tool/round scraper",
`Typology` == "doublenotch scraper" ~ "tool/double notch scraper",
`Typology` == "corerejuvention (core tablet?)" ~ "core/core tablet",
`Typology` == "truncationاریبب" ~ "tool/truncated piece",
`Typology` == "retouchedpiece (side scraper)" ~ "tool/side scraper",
`Typology` == "retochedpice" ~ "tool/retouched piece",
`Typology` == "truncation/notch" ~ "tool/truncated piece-notch",
`Typology` == "doublealternate scraper" ~ "tool/double side scraper",
`Typology` == "awl/ inverse notch" ~ "tool/notch",
`Typology` == "retouchedpiece (alternate scraper?)" ~ "tool/double side scraper",
`Typology` == "inverseside scraper" ~ "tool/side scraper",
`Typology` == "usedcore rejuvention" ~ "core/rejuvenation piece",
`Typology` == "coreside rejuvention" ~ "core/rejuvenation piece",
`Typology` == "coreplatform rejuvention flake" ~ "core/rejuvenation piece",
`Typology` == "corerejuvention platform" ~ "core/rejuvenation piece",
`Typology` == "coreside rejuvention blade" ~ "core/rejuvenation piece",
`Typology` == "coreside rejuvention blade??" ~ "core/rejuvenation piece",
`Typology` == "coreedge rejuvention" ~ "core/rejuvenation piece",
`Typology` == "coreedge rejivention" ~ "core/rejuvenation piece",
`Typology` == "retouchedpice (side scraper?)" ~ "tool/side scraper" ,
`Typology` == "scraper" ~ "tool/side scraper",
`Typology` == "sickleblade" ~ "tool/sickle shine",
`Typology` == "coretool (scraper)" ~ "tool/scraper-on core piece",
`Typology` == "retouchedpiece (scraper)" ~ "tool/side scraper",
`Typology` == "inversedenticulate?" ~ "tool/denticulate",
`Typology` == "retouchedpiece (scraper?)" ~ "tool/side scraper",
`Typology` == "coreside rejuvention flake" ~ "core/rejuvenation piece",
`Typology` == "truncation/endscraper" ~ "tool/endscraper on truncated piece",
`Typology` == "retouchedpice(double side scraper?)" ~ "tool/double side scraper",
`Typology` == "doublescraper" ~ "tool/double side scraper",
`Typology` == "dendiculate" ~ "tool/denticulate",
`Typology` == "double-scraper" ~ "tool/double side scraper",
`Typology` == "pyramidalcore" ~ "core/pyramid",
`Typology` == "bulletcore" ~ "core/bullet",
`Typology` == "corerejuvention" ~ "core/rejuvenation piece",
`Typology` == "pyrmidalcore" ~ "core/pyramid",
`Typology` == "corepreperation" ~ "core/core preparation piece",
`Typology` == "crested" ~ "core/crested bladelet",
`Typology` == "preperationblade" ~ "core/core preperation",
`Typology` == "burin" ~ "tool/burin",
`Typology` == "serrateddenticulate" ~ "tool/serrated scraper",
`Typology` == "saw:serrated denticulate" ~ "tool/serrated scraper",
`Typology` == "serratedused" ~ "tool/serrated scraper",
`Typology` == "corepreeration" ~ "tool/core preparation piece",
`Typology` == "coreprepearation" ~ "tool/core preparation piece",
`Typology` == "awl" ~ "tool/perforator-awl",
`Typology` == "notch.inverse" ~ "tool/notch",
`Typology` == "point.notch" ~ "tool/perforator-point;notch",
`Typology` == "inversescraper" ~ "tool/side scraper",
`Typology` == "roundendscraper" ~ "tool/round scraper",
`Typology` == "alternate.scraper" ~ "tool/double side scraper",
`Typology` == "convergentscraper/disc scraper" ~ "tool/scraper-convergent scraper",
`Typology` == "serratedside scraper" ~ "tool/serrated scraper",
`Typology` == "debri" ~ "NA/NA",
`Typology` == "distalpart of a drill" ~ "tool/perforator-drill",
`Typology` == "corepreperation?" ~ "core/core preparation piece",
`Typology` == "preformend of a borer" ~ "tool/perforator-borer; preform",
`Typology` == "used" ~ "tool/used",
`Typology` == "distalend of a inverse sidescraper" ~ "tool/side scraper",
`Typology` == "retouchedblade" ~ "tool/retouched piece",
`Typology` == "drill" ~ "tool/perforator-drill",
`Typology` == "corerejuvention tablet" ~ "core/core tablet",
`Typology` == "bladeletcore" ~ "core/pyramid",
`Typology` == "flake-bladecore" ~ "core/mixed",
`Typology` == "bladelet-corerejuvention" ~ "core/rejuvenation piece",
`Typology` == "bladelet-corefragment" ~ "core/core fragment",
`Typology` == "pointedused" ~ "tool/perforator-point",
`Typology` == "microburin" ~ "tool/microburin",
`Typology` == "bladeletcore fragment" ~ "core/core fragment",
`Typology` == "rejuventionface flake" ~ "core/rejuvenation piece",
`Typology` == "corepreperation flake" ~ "core/core preparation piece",
`Typology` == "corerejuvention flake" ~ "core/rejuvenation piece",
`Typology` == "unfinished pyramid core" ~ "core/pyramid",
`Typology` == "bladeletcoretablet" ~ "core/core tablet",
`Typology` == "bladeletcore rejuvention" ~ "core/rejuvenation piece",
`Typology` == "debitage" ~ "NA/NA",
`Typology` == "bladeletcore rejuvention" ~ "core/rejuvenation piece",
`Typology` == "inverseserrated scraper" ~ "tool/serrated scraper",
`Typology` == "backedknife" ~ "tool/backed knife",
`Typology` == "corepreparation" ~ "core/core preparation piece",
`Typology` == "primaryflake" ~ "core/primary flake",
`Typology` == "pointedconvergent scraper on bladelet" ~ "tool/perforator-point",
`Typology` == "trie" ~ "NA/NA",
`Typology` == "part of core tablet" ~ "core/core tablet",
`Typology` == "zaviedar" ~ "NA/NA",
`Typology` == "convergentscraper" ~ "tool/convergent scraper",
`Typology` == "preparationflake" ~ "core/core preparation piece",
`Typology` == "atypicalborer" ~ "tool/perforator-borer",
`Typology` == "naturalybacked knife" ~ "tool/backed knife-naturally backed knife",
`Typology` == "pyramidbladelet core" ~ "core/pyramid",
`Typology` == "flatbladelet core" ~ "core/flat",
`Typology` == "bladecore" ~ "core/pyramid",
`Typology` == "bulletbladelet core" ~ "core/bullet",
`Typology` == "coerejuvention flake" ~ "core/rejuvenation piece",
`Typology` == "finishedbladelet core" ~ "core/bullet",
`Typology` == "failed pyramid core?" ~ "core/pyramid",
`Typology` == "pyramidplain bladelet core" ~ "core/pyramid",
`Typology` == "coeon flake" ~ "core/core on flake",
`Typology` == "coeejuvention flake" ~ "core/rejuvenation piece",
`Typology` == "bladeletcoe rejuvention tablet?" ~ "core/core tablet",
`Typology` == "pyramidcore" ~ "core/pyramid",
`Typology` == "bladeletcore tablet" ~ "core/core tablet",
`Typology` == "pyramidbladeleet core" ~ "core/pyramid",
`Typology` == "flake" ~ "NA/NA",
`Typology` == "serrated" ~ "tool/serrated scraper",
`Typology` == "curvedretouched piece" ~ "tool/retouched piece",
`Typology` == "pyramidalbladelet core" ~ "core/pyramid",
`Typology` == "multidirectionalcore fragment" ~ "core/multidirectional core fragment",
`Typology` == "unidirectionalblade? core fragent" ~ "core/pyramid",
`Typology` == "backed/corerejuvention" ~ "tool/backed knife",
`Typology` == "unidirectionalbladelet core" ~ "core/pyramid",
`Typology` == "unifacialbalde core fragment?" ~ "core/pyramid",
`Typology` == "flakedetached from a bladelet core" ~ "core/core preparation piece",
`Typology` == "corepreparation tablet" ~ "core/core tablet",
`Typology` == "bladeletcore fragent" ~ "core/core fragment-pyramid",
`Typology` == "alternatescraper??" ~ "tool/double side scraper",
`Typology` == "endscraper.onrejuvention" ~ "core/rejuvenation piece",
`Typology` == "inverseserrated" ~ "tool/serrated scraper",
`Typology` == "patination.omitted" ~ "NA/NA",
`Typology` == "trapze" ~ "tool/geometric-triangle",
`Typology` == "trapzoid" ~ "tool/geometric-triangle",
`Typology` == "borer.drill" ~ "tool/perforator-drill",
`Typology` == "serraed" ~ "tool/serrated scraper",
`Typology` == "bladeletcore on a flake" ~ "core/core on flake",
`Typology` == "geofact" ~ "NA/NA",
`Typology` == "denticulateborer?" ~ "tool/perforator-borer;denticulate",
`Typology` == "sideborer-denticulate" ~ "tool/perforator-borer;denticulate",
`Typology` == "borer.awl" ~ "tool/perforator-awl",
`Typology` == "roundscraper" ~ "tool/round scraper",
`Typology` == "truncationon a bladelet core" ~ "tool/truncated piece",
`Typology` == "truncation.notch" ~ "tool/truncated piece;notch",
`Typology` == "backed-denticulate" ~ "tool/backed;denticulate",
`Typology` == "brokendrill" ~ "tool/perforator-drill",
`Typology` == "drillbroken" ~ "tool/perforator-drill",
`Typology` == "point/broken drill" ~ "tool/perforator-point",
`Typology` == "brokendrill?" ~ "tool/perforator-drill",
`Typology` == "partialyserrated" ~ "tool/serrated scraper",
`Typology` == "naturallybacked" ~ "tool/backed knife-naturally backed knife",
`Typology` == "transversescraper" ~ "tool/transverse scraper",
`Typology` == "naturalybacked" ~ "tool/backed knife-naturally backed knife",
`Typology` == "awl-notch" ~ "tool/perforator-awl",
`Typology` == "psedulevalois" ~ "tool/psedulevalois flake",
`Typology` == "alternatingdenticulate" ~ "tool/denticulate",
`Typology` == "usedcore fragment" ~ "tool/core tool-used core fragment",
`Typology` == "multidirectionalmicroflake core" ~ "core/multidirectional flake core",
`Typology` == "mixedpyramidal core" ~ "core/pyramid",
`Typology` == "usedbladecore fragment" ~ "tool/core tool-used core fragment",
`Typology` == "multidirectionalbladelet core fragment" ~ "core/multidirectional bladelet core",
`Typology` == "unidirectionalbladelet core.cylinder" ~ "core/prismatic",
`Typology` == "pyrymedalmixed core" ~ "core/pyramid",
`Typology` == "pyramedial/bullet core" ~ "core/bullet",
`Typology` == "corefragent" ~ "core/core fragment",
`Typology` == "pyramedialbladelet core fragment" ~ "core/pyramid",
`Typology` == "unidirectionalbladelet core fragment" ~ "core/pyramid",
`Typology` == "unifacialunidirectional bladelet core" ~ "core/pyramid",
`Typology` == "unidirectionalblade core" ~ "core/pyramid",
`Typology` == "pyramidalbladelet core fragment" ~ "core/pyramid",
`Typology` == "corerejuvention?" ~ "core/rejuvenation piece",
`Typology` == "flatburin? point?" ~ "tool/flat burin",
`Typology` == "primaryblade" ~ "core/primary blade",
`Typology` == "trihedralgeometric" ~ "tool/geometric-triangle",
`Typology` == "lunate" ~ "tool/geometric-lunate",
`Typology` == "corepaltform rejuvention flake" ~ "core/rejuvenation piece",
`Typology` == "pressurebladelet core /semi flat" ~ "core/pyramid",
`Typology` == "failedpercussion blade core/semi pyramedal" ~ "core/pyramid",
`Typology` == "percussionbladelet core/unidirectional" ~ "core/pyramid-percussion",
`Typology` == "percussion.unidirectional.blade-flakecore" ~ "core/mixed-percussion",
`Typology` == "obliqueretouched bladelet" ~ "tool/retouched piece",
`Typology` == "percussionunidirectional pyramidal bladelet core" ~ "core/pyramid",
`Typology` == "lunategeometric" ~ "tool/geometric-lunate",
`Typology` == "awl on a core rejuvention" ~ "tool/perforator-awl on core rejuvenation piece",
`Typology` == "truncated" ~ "tool/truncated piece",
`Typology` == "multiplenotch" ~ "tool/notch",
`Typology` == "dishedconvergent bladelet" ~ "tool/convergent scraper",
`Typology` == "bipolarpercussion blade-bladelet core" ~ "core/bipolar-percussion",
`Typology` == "bladeletbullet core" ~ "core/bullet",
`Typology` == "alternatingserrated" ~ "tool/serrated scraper",
`Typology` == "shaplesscore" ~ "core/shapeless",
`Typology` == "corepreparation?" ~ "core/core preparation piece",
`Typology` == "obliqueretouched" ~ "tool/retouched piece",
`Typology` == "corepreparation flake" ~ "core/core preparation piece",
`Typology` == "backeddenticulate" ~ "tool/backed;denticulate",
`Typology` == "awlnotch" ~ "tool/perforator-awl;notch",
`Typology` == "scraperburin?" ~ "tool/burin;scraper",
`Typology` == "notchround scraper" ~ "tool/round scraper;notch",
`Typology` == "corerejuvention tablet round scraper" ~ "tool/round scraper on core tablet",
`Typology` == "alternatescraper" ~ "tool/double side scraper",
`Typology` == "coreplatform preperation flake" ~ "core/rejuvenation piece",
`Typology` == "coreplatform rejuvention tablet" ~ "core/core tablet",
`Typology` == "brokenpyramidal core bladelet" ~ "core/pyramid",
`Typology` == "pyramidalbladelet core/semi bullet?" ~ "core/bullet",
`Typology` == "coreside rejuvention flake?" ~ "core/rejuvenation piece-side",
`Typology` == "unidirectionalpressure bladelet core/unifacila" ~ "core/pyramid",
`Typology` == "coreplatform rejuvention tablet/or multidirectional core" ~ "core/rejuvenation piece",
`Typology` == "bulletbladlet core" ~ "core/bullet",
`Typology` == "cylinderbipolar bladelet core" ~ "core/prismatic",
`Typology` == "backedknife/core platform rejuvenation" ~ "tool/backed knife",
`Typology` == "flatunifacial bladelet core" ~ "core/flat",
`Typology` == "coreprepration flake" ~ "core/core preparation piece",
`Typology` == "coreplatform preperation" ~ "core/core preparation piece-platform",
`Typology` == "borerpreform" ~ "tool/perforator-borer",
`Typology` == "rejuvention" ~ "core/rejuvenation piece",
`Typology` == "borerpreform?" ~ "tool/perforator-borer",
`Typology` == "inversnotch" ~ "tool/notch",
`Typology` == "alternateconvergent" ~ "tool/convergent scraper",
`Typology` == "unidirectionalbladelet/flake-blade core" ~ "core/mixed",
`Typology` == "unidirectionalmixed core" ~ "core/mixed",
`Typology` == "unidirectionalflat bladelet core" ~ "core/flat",
`Typology` == "" ~ "NA-NA",
`Typology` == "na" ~ "NA-NA",
`Typology` == "bladelet-corerejuvention" ~ "core/rejuvenation piece",
`Typology` == "bladelet-corefragment" ~ "core/core fragment",
`Typology` == "pointedused" ~ "tool/perforator-point",
`Typology` == "microburin" ~ "tool/microburin",
`Typology` == "bladeletcore fragment" ~ "core/core fragment",
`Typology` == "rejuventionface flake" ~ "core/rejuvenation piece",
`Typology` == "corepreperation flake" ~ "core/core preparation piece",
`Typology` == "corerejuvention flake" ~ "core/rejuvenation piece",
`Typology` == "unfinished pyramid core" ~ "core/pyramid",
`Typology` == "bladeletcoretablet" ~ "core/core tablet",
`Typology` == "bladeletcore rejuvention" ~ "core/rejuvenation piece",
`Typology` == "debitage" ~ "NA/NA",
`Typology` == "bladeletcore rejuvention" ~ "core/rejuvenation piece",
`Typology` == "inverseserrated scraper" ~ "tool/serrated scraper",
`Typology` == "backedknife" ~ "tool/backed knife",
`Typology` == "corepreparation" ~ "core/core preparation piece",
`Typology` == "primaryflake" ~ "core/primary flake",
`Typology` == "pointedconvergent scraper on bladelet" ~ "tool/perforator-point",
`Typology` == "trie" ~ "NA/NA",
`Typology` == "part of core tablet" ~ "core/core tablet",
`Typology` == "zaviedar" ~ "NA/NA",
`Typology` == "convergentscraper" ~ "tool/convergent scraper",
`Typology` == "preparationflake" ~ "core/core preparation piece",
`Typology` == "atypicalborer" ~ "tool/perforator-borer",
`Typology` == "naturalybacked knife" ~ "tool/backed knife-naturally backed knife",
`Typology` == "pyramidbladelet core" ~ "core/pyramid",
`Typology` == "flatbladelet core" ~ "core/flat",
`Typology` == "bladecore" ~ "core/pyramid",
`Typology` == "bulletbladelet core" ~ "core/bullet",
`Typology` == "coerejuvention flake" ~ "core/rejuvenation piece",
`Typology` == "finishedbladelet core" ~ "core/bullet",
`Typology` == "failed pyramid core?" ~ "core/pyramid",
`Typology` == "pyramidplain bladelet core" ~ "core/pyramid",
`Typology` == "coeon flake" ~ "core/core on flake",
`Typology` == "coeejuvention flake" ~ "core/rejuvenation piece",
`Typology` == "bladeletcoe rejuvention tablet?" ~ "core/core tablet",
`Typology` == "pyramidcore" ~ "core/pyramid",
`Typology` == "bladeletcore tablet" ~ "core/core tablet",
`Typology` == "pyramidbladeleet core" ~ "core/pyramid",
`Typology` == "flake" ~ "NA/NA",
`Typology` == "serrated" ~ "tool/serrated scraper",
`Typology` == "curvedretouched piece" ~ "tool/retouched piece",
`Typology` == "pyramidalbladelet core" ~ "core/pyramid",
`Typology` == "multidirectionalcore fragment" ~ "core/multidirectional core fragment",
`Typology` == "unidirectionalblade? core fragent" ~ "core/pyramid",
`Typology` == "backed/corerejuvention" ~ "tool/backed knife",
`Typology` == "unidirectionalbladelet core" ~ "core/pyramid",
`Typology` == "unifacialbalde core fragment?" ~ "core/pyramid",
`Typology` == "flakedetached from a bladelet core" ~ "core/core preparation piece",
`Typology` == "corepreparation tablet" ~ "core/core tablet",
`Typology` == "bladeletcore fragent" ~ "core/core fragment-pyramid",
`Typology` == "alternatescraper??" ~ "tool/double side scraper",
`Typology` == "endscraper.onrejuvention" ~ "core/rejuvenation piece",
`Typology` == "inverseserrated" ~ "tool/serrated scraper",
`Typology` == "patination.omitted" ~ "NA/NA",
`Typology` == "trapze" ~ "tool/geometric-triangle",
`Typology` == "trapzoid" ~ "tool/geometric-triangle",
`Typology` == "borer.drill" ~ "tool/perforator-drill",
`Typology` == "serraed" ~ "tool/serrated scraper",
`Typology` == "bladeletcore on a flake" ~ "core/core on flake",
`Typology` == "geofact" ~ "NA/NA",
`Typology` == "denticulateborer?" ~ "tool/perforator-borer;denticulate",
`Typology` == "sideborer-denticulate" ~ "tool/perforator-borer;denticulate",
`Typology` == "borer.awl" ~ "tool/perforator-awl",
`Typology` == "roundscraper" ~ "tool/round scraper",
`Typology` == "truncationon a bladelet core" ~ "tool/truncated piece",
`Typology` == "truncation.notch" ~ "tool/truncated piece;notch",
`Typology` == "backed-denticulate" ~ "tool/backed;denticulate",
`Typology` == "brokendrill" ~ "tool/perforator-drill",
`Typology` == "drillbroken" ~ "tool/perforator-drill",
`Typology` == "point/broken drill" ~ "tool/perforator-point",
`Typology` == "brokendrill?" ~ "tool/perforator-drill",
`Typology` == "partialyserrated" ~ "tool/serrated scraper",
`Typology` == "naturallybacked" ~ "tool/backed knife-naturally backed knife",
`Typology` == "transversescraper" ~ "tool/transverse scraper",
`Typology` == "naturalybacked" ~ "tool/backed knife-naturally backed knife",
`Typology` == "awl-notch" ~ "tool/perforator-awl",
`Typology` == "psedulevalois" ~ "tool/psedulevalois flake",
`Typology` == "alternatingdenticulate" ~ "tool/denticulate",
`Typology` == "usedcore fragment" ~ "tool/core tool-used core fragment",
`Typology` == "multidirectionalmicroflake core" ~ "core/multidirectional flake core",
`Typology` == "mixedpyramidal core" ~ "core/pyramid",
`Typology` == "usedbladecore fragment" ~ "tool/core tool-used core fragment",
`Typology` == "multidirectionalbladelet core fragment" ~ "core/multidirectional bladelet core",
`Typology` == "unidirectionalbladelet core.cylinder" ~ "core/prismatic",
`Typology` == "pyrymedalmixed core" ~ "core/pyramid",
`Typology` == "pyramedial/bullet core" ~ "core/bullet",
`Typology` == "corefragent" ~ "core/core fragment",
`Typology` == "pyramedialbladelet core fragment" ~ "core/pyramid",
`Typology` == "unidirectionalbladelet core fragment" ~ "core/pyramid",
`Typology` == "unifacialunidirectional bladelet core" ~ "core/pyramid",
`Typology` == "unidirectionalblade core" ~ "core/pyramid",
`Typology` == "pyramidalbladelet core fragment" ~ "core/pyramid",
`Typology` == "corerejuvention?" ~ "core/rejuvenation piece",
`Typology` == "flatburin? point?" ~ "tool/flat burin",
`Typology` == "primaryblade" ~ "core/primary blade",
`Typology` == "trihedralgeometric" ~ "tool/geometric-triangle",
`Typology` == "lunate" ~ "tool/geometric-lunate",
`Typology` == "corepaltform rejuvention flake" ~ "core/rejuvenation piece",
`Typology` == "pressurebladelet core /semi flat" ~ "core/pyramid",
`Typology` == "failedpercussion blade core/semi pyramedal" ~ "core/pyramid",
`Typology` == "percussionbladelet core/unidirectional" ~ "core/pyramid-percussion",
`Typology` == "percussion.unidirectional.blade-flakecore" ~ "core/mixed-percussion",
`Typology` == "obliqueretouched bladelet" ~ "tool/retouched piece",
`Typology` == "percussionunidirectional pyramidal bladelet core" ~ "core/pyramid",
`Typology` == "lunategeometric" ~ "tool/geometric-lunate",
`Typology` == "awl on a core rejuvention" ~ "tool/perforator-awl on core rejuvenation piece",
`Typology` == "truncated" ~ "tool/truncated piece",
`Typology` == "multiplenotch" ~ "tool/notch",
`Typology` == "dishedconvergent bladelet" ~ "tool/convergent scraper",
`Typology` == "bipolarpercussion blade-bladelet core" ~ "core/bipolar-percussion",
`Typology` == "bladeletbullet core" ~ "core/bullet",
`Typology` == "alternatingserrated" ~ "tool/serrated scraper",
`Typology` == "shaplesscore" ~ "core/shapeless",
`Typology` == "corepreparation?" ~ "core/core preparation piece",
`Typology` == "obliqueretouched" ~ "tool/retouched piece",
`Typology` == "corepreparation flake" ~ "core/core preparation piece",
`Typology` == "backeddenticulate" ~ "tool/backed;denticulate",
`Typology` == "awlnotch" ~ "tool/perforator-awl;notch",
`Typology` == "scraperburin?" ~ "tool/burin;scraper",
`Typology` == "notchround scraper" ~ "tool/round scraper;notch",
`Typology` == "corerejuvention tablet round scraper" ~ "tool/round scraper on core tablet",
`Typology` == "alternatescraper" ~ "tool/double side scraper",
`Typology` == "coreplatform preperation flake" ~ "core/rejuvenation piece",
`Typology` == "coreplatform rejuvention tablet" ~ "core/core tablet",
`Typology` == "brokenpyramidal core bladelet" ~ "core/pyramid",
`Typology` == "pyramidalbladelet core/semi bullet?" ~ "core/bullet",
`Typology` == "coreside rejuvention flake?" ~ "core/rejuvenation piece-side",
`Typology` == "unidirectionalpressure bladelet core/unifacila" ~ "core/pyramid",
`Typology` == "coreplatform rejuvention tablet/or multidirectional core" ~ "core/rejuvenation piece",
`Typology` == "bulletbladlet core" ~ "core/bullet",
`Typology` == "cylinderbipolar bladelet core" ~ "core/prismatic",
`Typology` == "backedknife/core platform rejuvenation" ~ "tool/backed knife",
`Typology` == "flatunifacial bladelet core" ~ "core/flat",
`Typology` == "coreprepration flake" ~ "core/core preparation piece",
`Typology` == "coreplatform preperation" ~ "core/core preparation piece-platform",
`Typology` == "borerpreform" ~ "tool/perforator-borer",
`Typology` == "rejuvention" ~ "core/rejuvenation piece",
`Typology` == "borerpreform?" ~ "tool/perforator-borer",
`Typology` == "inversnotch" ~ "tool/notch",
`Typology` == "alternateconvergent" ~ "tool/convergent scraper",
`Typology` == "unidirectionalbladelet/flake-blade core" ~ "core/mixed",
`Typology` == "unidirectionalmixed core" ~ "core/mixed",
`Typology` == "unidirectionalflat bladelet core" ~ "core/flat",
`Typology` == "" ~ "",
`Typology` == "na" ~ "",
TRUE ~ `Typology`
)
) %>%
mutate(
typology_split = str_split(Typology, "/", simplify = TRUE),
`typology-tool-core` = typology_split[, 1],
tool_or_core = ifelse(str_starts(`typology-tool-core`, "tool"), "tool", "core"),
`tool-typology` = ifelse(tool_or_core == "tool", typology_split[, 2], NA),
`core-fragment` = ifelse(tool_or_core == "core", typology_split[, 2], NA)
) %>%
# remove temporary columns
select(-typology_split,-tool_or_core)
# BM: still some typos in there
# rev(sort(table((tl4$`tool-typology`))))
# rev(sort(table((tl4$`core-fragment`))))# refine the table
tl_final <- tl4 %>%
dplyr::rename(
blank = Blank2,
`sickle shine` = shine2,
length = `Length (mm)` ,
width = `Width (mm)`,
thickness = `Thickness (mm)`,
typology = Typology,
utilization = Utilization,
retouch = Retouch,
blank = Blank2,
`blank part` = `Blank_part`,
`bulb thickness` = `Bulb Thickness (mm)`,
`platform thickness` = `Platform Thickness (mm)`,
`platform length` = `platform Length (mm)`,
eraillure = Eraillure ,
cortex = `Cortex (%)`) %>%
mutate(area_unit = paste0(toupper(area), "_", chronological_unit)) %>%
relocate(area_unit, .after = chronological_unit) %>%
relocate(grouped_level, .after = area_unit) %>%
select(lithic_id,
TA,
area,
chronological_unit,
area_unit,
grouped_level,
cortex,
depth, upper, lower, midpoint,
`length`, `width`, `thickness`,
typology,
utilization,
`sickle shine`,
retouch,
`typology-tool-core`,
`tool-typology`,
blank, `blank part`,
`core-typology`, `core-fragment`,`core-technology`,
cortex) %>%
# Update the 'typology-tool-core' column based on 'Retouch'
mutate(
`typology-tool-core` = case_when(
retouch == 1 ~ "tool",
utilization == 1 ~ "tool",
`sickle shine` == 1 ~ "tool",
TRUE ~ `typology-tool-core`
)
) %>%
mutate(
`tool-typology` = case_when(
utilization == 1 ~ "utilized tool",
`sickle shine` == 1 ~ "sickle shine",
TRUE ~ `tool-typology`
)
) %>%
mutate(
`tool-typology` = case_when(
# If Retouch is 1 and tool-typology is NA
retouch == 1 & is.na(`tool-typology`) ~ "retouched piece",
`sickle shine` == 1 & is.na(`tool-typology`) ~ "sickle shine",
# For all other cases
TRUE ~ `tool-typology`
)
)
# BM: take a look at tool typology
# rev(sort(table(tl_final$`tool-typology`)))# List of columns that should be numeric
columns_to_convert <- c("cortex",
"upper",
"lower",
"midpoint",
"length",
"width",
"utilization",
"retouch",
"sickle shine")
# Convert each column to numeric
# BM: this is how I would convert those columns to numeric,
# I think it's easier to read and requires less typing
tl_final <-
tl_final %>%
mutate(across(all_of(columns_to_convert),
parse_number))
# check the structure to see if they have been converted
# str(tl_final)#set the value of utilization to NA only for the rows where `sickle shine` == 1.
tl_final <- tl_final %>%
rowwise() %>%
mutate(utilization = ifelse(is.na(`sickle shine`) | is.na(utilization),
utilization,
ifelse(`sickle shine` == 1 & utilization == 1,
NA_real_,
utilization))) %>%
ungroup() %>%
# make the number of `sickle shine` in column `sickle shine` match:
mutate(
`tool-typology` = case_when(
`sickle shine` == 1 ~ "sickle shine",
utilization == 1 ~ "utilized tool",
TRUE ~ `tool-typology`
)
)# Creating tooltypegroup
tl_final <- tl_final %>%
mutate(
tooltypegroup = case_when(
`tool-typology` %in%
c(
"end scraper",
"side scraper",
"double side scraper",
"convergent scraper",
"round scraper",
"perforator-convergent scraper",
"perforator-borer; preform",
"scraper-on core piece",
"endscraper on truncated piece",
"round scraper",
"transverse scraper",
"core tool-used core fragment",
"round scraper on core tablet"
) ~ "scraper",
`tool-typology` %in%
c(
"perforator-borer",
"perforator-drill",
"perforator-point",
"perforator-awl",
"perforator-point;notch",
"perforator-awl on core rejuvenation piece",
"perforator-awl;notch",
"perforator-borer;denticulate"
) ~ "Perforator",
`tool-typology` %in%
c(
"backed knife",
"backed knife-naturally backed knife",
"backed;denticulate"
) ~ "backed pieces",
`tool-typology` %in% c(
"double notch",
"denticulate",
" denticulate",
"notch-denticulate",
"notch"
) ~ "denticulate-notch",
`tool-typology` %in% c(
"notch-side scraper",
"notch-end scraper",
"double notch scraper",
"round scraper;notch"
) ~ "scraper-notch",
`tool-typology` %in% c("geometric-triangle", "geometric-lunate") ~ "geometric",
`tool-typology` == "serrated scraper" ~ "serrated scraper",
`tool-typology` %in% c(
"truncated piece",
"truncated piece-notch",
"truncated piece;notch",
"notch;truncated piece"
) ~ "truncated pieces",
# Represents NA group
`tool-typology` %in% c("core preparation piece", "used", "psedulevalois flake") ~ NA_character_,
`tool-typology` %in% c("burin", "flat burin", "burin;scraper", "burin-notch-scraper") ~ "burin",
`tool-typology` == "microburin" ~ "microburin",
`tool-typology` == "retouched piece" ~ "retouched piece",
`tool-typology` == "utilized tool" ~ "utilized tool",
`tool-typology` == "sickle shine" ~ "sickle shine",
#classify any remaining values as NA
TRUE ~ NA_character_
)
)
# Checking the unique values of tooltypegroup
# rev(sort(table(tl_final$tooltypegroup)))# Define the patterns to search for
patterns <- c("denticulate-notch",
"retouched piece",
"scraper",
"Perforator",
"serrated scraper",
"backed pieces",
"truncated pieces",
"burin",
"geometric",
"scraper-notch",
"microburin")
# Update the `retouch` column based on the `tooltypegroup` column
tl_final <- tl_final %>%
mutate(retouch = ifelse(str_detect(tooltypegroup,
str_c(patterns,
collapse = "|")),
1, retouch))
# View the first few rows to confirm
# head(tl_final)
# rev(sort(table(tl_final$tooltypegroup)))
# rev(sort(table(tl_final$retouch)))tl_final <- tl_final %>%
mutate(`core-fragment` = if_else(!is.na(`core-typology`),
NA_character_,
`core-fragment`)) %>%
mutate(`core-fragment` = if_else(!is.na(`core-typology`),
NA_character_,
`core-fragment`)) %>%
mutate(
`core-fragment` = case_when(
`core-fragment` == "rejuvenation piece" ~ "rejuvenation piece",
`core-fragment` == "rejuvention piece-side" ~ "rejuvenation piece",
`core-fragment` == "rejuvenation piece-side" ~ "rejuvenation piece",
`core-fragment` == "core preparation piece-platform" ~ "core tablet",
`core-fragment` == "core preparation piece-platform" ~ "core tablet",
`core-fragment` == "core platform rejuvention" ~ "core tablet",
`core-fragment` == "core platform rejuvention " ~ "core tablet",
`core-fragment` == "core preparation" ~ "rejuvenation piece",
`core-fragment` == "core preparation piece" ~ "rejuvenation piece",
`core-fragment` == "core preperation" ~ "rejuvenation piece",
`core-fragment` == "pyramid" ~ "pyramid",
`core-fragment` == "pyramid core" ~ "pyramid",
`core-fragment` == "pyramid-unidirectional" ~ "pyramid",
`core-fragment` == "core fragment-pyramid" ~ "pyramid",
`core-fragment` == "cylinder" ~ "cylinder/prismatic",
`core-fragment` == "prismatic" ~ "cylinder/prismatic",
`core-fragment` == "shapeless" ~ "shapeless",
`core-fragment` == "multidirectional core fragment" ~ "shapeless",
`core-fragment` == "multidirectional flake core" ~ "shapeless",
`core-fragment` == "multidirectional bladelet core" ~ "shapeless",
`core-fragment` == "mixed core" ~ "shapeless",
`core-fragment` == "mixed-percussion" ~ "shapeless",
`core-fragment` == "mixed" ~ "shapeless",
`core-fragment` == ("bipolar-percussion") ~ "bipolar",
`core-fragment` == "flat" ~ "flat",
`core-fragment` == "core on flake" ~ "core on flake",
`core-fragment` == "bullet" ~ "bullet",
`core-fragment` == "NA" ~ "",
TRUE ~ `core-fragment`
)
) %>%
mutate(
core = case_when(
`core-fragment` %in% c(
"pyramid",
"cylinder/prismatic",
"core fragment",
"cylinder/prismatic",
"bullet",
"flat",
"core on flake",
"bipolar",
"mixed core",
"mixed-percussion",
"mixed",
"bipolar-percussion",
"flat",
"core on flake",
"bullet",
"pyramid",
"flat",
"cylinder/prismatic ",
"bipolar ",
"shapeless ",
"bullet "
) ~ `core-fragment`,
TRUE ~ NA_character_
),
corefrag = case_when(
`core-fragment` %in% c(
"rejuvenation piece",
"core tablet",
"primary flake",
"primary blade",
"crested bladelet",
"core preperation",
"crested bladelet" ,
"primary flake" ,
"primary blade",
"core fragment "
) ~ `core-fragment`,
TRUE ~ NA_character_
)
) %>%
# Convert empty strings to NA in `core-fragment` column
mutate(`core-fragment` = if_else(`core-fragment` == "", NA_character_, `core-fragment`)) %>%
# Convert "pyramid-percussion" to "pyramid" in `core-fragment` column
mutate(
`core-fragment` =
if_else(
`core-fragment` == "pyramid-percussion",
"pyramid",
`core-fragment`
)
) %>%
# Update existing `core` column with selected values from `core-fragment` column
mutate(core = if_else(
`core-fragment` %in%
c(
"shapeless",
"pyramid",
"cylinder/prismatic",
"flat",
"bullet",
"core on flake",
"pyramid"
),
`core-fragment`,
core
)) %>%
# Add 'core tablet' and 'core fragment' from `core-fragment` to `corefrag`
mutate(
corefrag = case_when(
`core-fragment` == "core tablet" ~ "core tablet",
`core-fragment` == "core fragment" ~ "core fragment",
TRUE ~ corefrag
)
) %>%
# Transfer 'rejuvenation piece' and 'core fragment' from `core-typology` to `corefrag`
mutate(
corefrag = case_when(
`core-typology` == "rejuvenation piece" ~ "rejuvenation piece",
`core-typology` == "core fragment" ~ "core fragment",
TRUE ~ corefrag
)
) %>%
# Remove 'rejuvenation piece' and 'core fragment' from `core-typology`
mutate(`core-typology` = if_else(
`core-typology` %in% c("rejuvenation piece", "core fragment"),
NA_character_,
`core-typology`
)) %>%
# Update the 'blank' column based on conditions in the 'core-fragment' column
mutate(blank = if_else(
`core-fragment` %in% c(
"core fragment",
"core tablet",
"rejuvenation piece",
"pyramid",
"crested bladelet",
"shapeless",
"primary flake",
"flat",
"bullet",
"core on flake",
"cylinder/prismatic",
"primary blade",
"rejuvenation piece-side",
"core platform rejuvention"
),
NA_character_,
blank
))
# take a look
# rev(sort(table(tl_final$core)))
# rev(sort(table(tl_final$corefrag)))
# rev(sort(table(tl_final$`core-fragment`)))
# rev(sort(table(tl_final$`core-typology`)))
# rev(sort(table(tl_final$blank)))Summary tables of the lithic assemblages
Basic typological classes by excavation area
# Create a summary table
summary_table_area <- tl_final %>%
group_by(area) %>%
dplyr::summarise(
`Cores (n)` = sum((!is.na(`core-typology`) & `core-typology` != "") |
(!is.na(core) & core != ""), na.rm = TRUE), # Summing variables from both columns
`Core rejuvenations pieces (n)` = sum(!is.na(corefrag) &
corefrag != ""),
`Blade (n)` = sum(blank == "blade", na.rm = TRUE),
`Flake (n)` = sum(blank == "flake", na.rm = TRUE),
`Bladelet (n)` = sum(blank == "bladelet", na.rm = TRUE),
`Retouched Tools (n)` = sum(retouch == 1, na.rm = TRUE),
`Utilized (n)` = sum(utilization == 1, na.rm = TRUE),
`Sickle Shine (n)` = sum(`sickle shine` == 1, na.rm = TRUE)
)
# Filter the data to include only the areas 'ta', 'd1', and 'tp1'
tl_final_area <- tl_final %>%
filter(area %in% c("ta", "d1", "tp1"))
summary_table_area_filtered <-
summary_table_area %>%
dplyr::filter(area %in% c("ta", "d1", "tp1"))
# BM: export this table as a CSV to paste into the
# drafting document to prepare for submission
write_csv(summary_table_area_filtered,
here::here("data/derived-data/tbl-001-summary_table_area_filtered.csv"))
# BM: this is table 1 in the manuscript
knitr::kable(summary_table_area_filtered,
caption = "Summary of lithics in the main areas")| area | Cores (n) | Core rejuvenations pieces (n) | Blade (n) | Flake (n) | Bladelet (n) | Retouched Tools (n) | Utilized (n) | Sickle Shine (n) |
|---|---|---|---|---|---|---|---|---|
| d1 | 6 | 4 | 33 | 5 | 109 | 21 | 5 | 1 |
| ta | 142 | 81 | 708 | 151 | 2245 | 408 | 282 | 48 |
| tp1 | 2 | 8 | 52 | 29 | 217 | 38 | 31 | 6 |
# chi-square test for different frequencies of tool type groups
# by area
summary_table_area_filtered_for_chi_square <-
summary_table_area_filtered %>%
pivot_longer(-area) %>%
pivot_wider(names_from = "area") %>%
select(-name)
chisq <-
chisq.test(summary_table_area_filtered_for_chi_square)
rownames(chisq$residuals) <-
summary_table_area_filtered %>%
pivot_longer(-area) %>%
pivot_wider(names_from = "area") %>%
pull(name) %>%
str_remove("\\(n\\)")
ggcorrplot(chisq$residuals,
method = 'circle') +
ggplot2::scale_fill_gradient2(
low = 'red',
high = 'royalblue',
mid = 'white',
midpoint = 0,
limit = c(-7, 11),
space = "Lab",
name = "Residual"
) +
coord_flip()
A Chi-square test on the frequency of major lithic types by excavation area reveals a significant difference between the areas (\(\chi^2\)(14, N = 4632) = 34.04, p = .002, V = .06). Figure XXX shows that there are fewer utlized pieces and flakes in d1 than expected, and more flakes and fewer cores and blades in tp1 than expected assuming a null hypothesis of no difference between the areas.
Techno-typological classes by excavation area
# Create a summary table for typology based on area
summary_table_tool_area <- tl_final %>%
filter(area %in% c("ta", "d1", "tp1")) %>%
filter(!is.na(tooltypegroup), tooltypegroup != "") %>% # Exclude rows where 'tooltypegroup' is NA or empty
group_by(area, tooltypegroup) %>% # Group the data by area and tooltypegroup
tally() %>% # Count the number of rows in each group
arrange(area, tooltypegroup) %>% # Arrange by area and tooltypegroup
spread(key = area,
value = n,
fill = 0) # Spread the 'area' column into multiple columns
# Add a "Total" column that sums each row
summary_table_tool_area <- summary_table_tool_area %>%
mutate(Total = rowSums(select(.,-tooltypegroup)))
total_row <- summary_table_tool_area %>%
select(-tooltypegroup) %>%
dplyr::summarise(across(everything(), \(x) sum(x, na.rm = TRUE))) %>%
mutate(tooltypegroup = "Total")
summary_table_tool_area <-
bind_rows(summary_table_tool_area, total_row)
# BM: export this table as a CSV to paste into the
# drafting document to prepare for submission
write_csv(summary_table_tool_area,
here::here("data/derived-data/tbl-002-summary_table_tool_area.csv"))
kable(
summary_table_tool_area,
col.names = c("Tools", "D1", "TA", "TP1", "Total"),
caption = "Tool Typology in the three main areas")| Tools | D1 | TA | TP1 | Total |
|---|---|---|---|---|
| backed pieces | 0 | 11 | 2 | 13 |
| burin | 2 | 8 | 1 | 11 |
| denticulate-notch | 4 | 110 | 7 | 121 |
| geometric | 3 | 2 | 0 | 5 |
| microburin | 0 | 4 | 0 | 4 |
| Perforator | 2 | 50 | 2 | 54 |
| retouched piece | 5 | 89 | 15 | 109 |
| scraper | 4 | 84 | 6 | 94 |
| scraper-notch | 0 | 4 | 0 | 4 |
| serrated scraper | 0 | 15 | 1 | 16 |
| sickle shine | 1 | 48 | 6 | 55 |
| truncated pieces | 1 | 10 | 0 | 11 |
| utilized tool | 5 | 282 | 31 | 318 |
| Total | 27 | 717 | 71 | 815 |
# chi-square test for different frequencies of tool type groups
# by area
summary_table_tool_area_for_chi_square <-
summary_table_tool_area %>%
filter(!tooltypegroup == "Total") %>%
select(d1, ta, tp1)
chisq <-
chisq.test(summary_table_tool_area_for_chi_square)
rownames(chisq$residuals) <-
summary_table_tool_area %>%
filter(!tooltypegroup == "Total") %>%
pull(tooltypegroup)
ggcorrplot(chisq$residuals,
method = 'circle') +
ggplot2::scale_fill_gradient2(
low = 'red',
high = 'royalblue',
mid = 'white',
midpoint = 0,
limit = c(-7, 11),
space = "Lab",
name = "Residual"
) +
coord_flip()
A Chi-square test on the frequency of tool type groups by excavation area reveals a significant difference between the areas (\(\chi^2\)(24, N = 815) = 74.95, p < .001, V = .21). Figure XXX shows that there are more geomeric pieces and burins in d1 than expected, and more backed and retouched pieces in tp1 than expected assuming a null hypothesis of no difference between the areas.
# Manually calculate the totals for each area and grand total
total_d1 <- sum(summary_table_tool_area$d1, na.rm = TRUE)
total_ta <- sum(summary_table_tool_area$ta, na.rm = TRUE)
total_tp1 <- sum(summary_table_tool_area$tp1, na.rm = TRUE)
grand_total <- total_d1 + total_ta + total_tp1
# Calculate the percentages for each cell based on the total count
summary_table_tool_area_percentage <- summary_table_tool_area %>%
mutate(
percent_d1 = round(d1 / total_d1 * 100, 1),
percent_ta = round(ta / total_ta * 100, 1),
percent_tp1 = round(tp1 / total_tp1 * 100, 1)
) %>%
# Add the total_percent column, calculating based on grand total
mutate(total_percent = round((d1 + ta + tp1) / grand_total * 100, 1))
# Select only the necessary columns (tooltypegroup, the percentage columns, and total_percent)
summary_table_tool_area_percentage <- summary_table_tool_area_percentage %>%
select(tooltypegroup, percent_d1, percent_ta, percent_tp1, total_percent)
# write the percentage table to a CSV file
write_csv(summary_table_tool_area_percentage,
here::here("data/derived-data/tbl-002-summary_table_tool_area_percentage.csv"))Combine lithic data with excavation data to prepare for WABI
# Create the 'label' column
tl_final_depth_area_unit <-
tl_final %>%
mutate(label1 = paste(area,
chronological_unit,
grouped_level,
sep = "_")) %>%
mutate(label2 = paste(area,
chronological_unit,
grouped_level,
upper,
lower,
sep = "_")) %>%
# we don't care about lithics with missing and incomplete
# excavation provenance, so drop those
filter(!str_detect(label1, "NA")) %>%
# so we can join this column ok
mutate(grouped_level = parse_number(grouped_level))
# BM: For the individual lithic data, what area/chrono-unit/grouped level
# combinations do we have? We only want to match those with the
# excavation data that we can calclate volume with.
lithics_unique_labels <-
tl_final_depth_area_unit %>%
pull(label2) %>%
unique() %>%
sort()
# BM: prepare excavation data here
excavation_data_volume <-
excavation_data %>%
mutate(thickness_of_excavation_unit = lower_depth - upper_depth) %>%
mutate(excavation_volume = excavation_dimension_1 *
excavation_dimension_2 *
thickness_of_excavation_unit / 100)
# BM: for the WABI plot, we have our primary analytical unit as
# excavation_area / chronological_unit / depth which is our label2
# variable, each row in the excavation_data_volume table is a
# unique combination of excavation_area / chronological_unit / depth
# BM: Now we subset the excavation data so we only look at the
# data that we need for the lithics, ie. we drop excavation data
# that has no corresponding lithics
tl_final_excavation_data_volume <-
excavation_data_volume %>%
filter(label2 %in% lithics_unique_labels) %>%
# now we join the excavation data to the individual lithic records
right_join(tl_final_depth_area_unit)
# get the counts of artefact types per ex-area/chrono-unit/depth
tl_final_excavation_data_volume_artefact_counts <-
tl_final_excavation_data_volume %>%
group_by(label2) %>%
dplyr::summarise(
blade_count = sum(blank == "blade", na.rm = TRUE),
flake_count = sum(blank == "flake", na.rm = TRUE),
bladelet_count = sum(blank == "bladelet", na.rm = TRUE),
tool_count = sum(retouch == 1,
na.rm = TRUE) + sum(utilization == 1,
na.rm = TRUE),
core_count = sum(!is.na(`core-typology`), na.rm = TRUE) + sum(!is.na(core), na.rm = TRUE),
core_rejuvenation_count = sum(!is.na(`corefrag`),
na.rm = TRUE),
retouched_tool_count = sum(retouch == 1,
na.rm = TRUE),
utilized_tool_count = sum(utilization == 1,
na.rm = TRUE),
shine_tool_count = sum(`sickle shine` == 1,
na.rm = TRUE),
tool_type_count = n_distinct(tooltypegroup),
excavation_volume = unique(excavation_volume)
) %>%
# BM: "total lithics" is everything except sickle shine,
# "retouch frequency" is retouched_tool_count / "total lithics"
# SS: I think "total lithics" would be the total of blade, flake,bladelet, core and core rejuvenation counts (as we already cound the tools in bladelet, blade, or flake)
rowwise() %>%
mutate(total_lithics = sum(blade_count,
flake_count,
bladelet_count,
core_count,
core_rejuvenation_count
)) %>%
mutate(retouch_frequency = retouched_tool_count / total_lithics)
# BM: get the total number of artefacts, number of retouched pieces, and
# artefact density. I think this gets us to something similar to the google
# sheet, the values are not exact, but I have no way to check how how
# calculated the values in the google sheet so
sum_depth_sheet <-
tl_final_excavation_data_volume_artefact_counts %>%
# some ex-area/chrono-unit/depth have no volume, so drop those
drop_na(excavation_volume) %>%
mutate(lithic_density = total_lithics / excavation_volume)Plot the WABI
library(ggpmisc)
library(ggrepel)
# Create the plot: WABI_Level_logscale
# here I do not consider those levels with a value 0 of retouch frequency.
filtered_data <-
sum_depth_sheet %>%
filter(lithic_density > 0 & retouch_frequency > 0) %>%
mutate(excavation_area = str_extract(label2, "[^_]+"))
WABI_Level <- ggplot(filtered_data,
aes(x = lithic_density,
y = retouch_frequency)) +
geom_point(aes(color = excavation_area,
shape = excavation_area),
size = 4) +
geom_smooth(method = "lm",
se = FALSE,
color = "blue",
linewidth = 0.5) +
# Add text labels based on 'label' column
# BM: this is useful for investigating and
# preparing, but not really informative
# for the reader, so we omit for publication
# geom_text_repel(aes(label = label2)) +
stat_poly_eq(aes(label = paste(stat(eq.label),
stat(rr.label),
stat(p.value.label),
sep = "~~~")),
formula = y ~ x,
parse = TRUE,
size = 5,
label.x = "right",
label.y = "bottom") +
labs(
x = "Lithic Volumetric Density",
y = "Retouch Frequency",
colour = "Excavation area",
shape = "Excavation area"
) +
scale_x_log10() +
scale_y_log10() +
theme_minimal() +
theme(
legend.position = c(.8,.3),
axis.text = element_text(size = 7),
axis.title = element_text(size = 10),
plot.title = element_text(size = 12)
)
# Print the plot to display it
WABI_Level
# BM: save this figure to paste into the
# drafting document to prepare for submission
ggsave(here::here("figures/fig-wabi-plot.jpg"),
h = 6,
w = 8)
Compute PCA
# PCA_Level: preparing data
# PCA_level: for PCA Bicho and Cascalheira considered these variables:
# - estimated area (as we calculated based on levels, should I consider the thickness?),
# - core frequency: core_count / total_lithics
# - blank frequency: (flake + blade + bladelet) / total_lithics
# - chip frequency: artefacts smaller than 1 cm (as we work on a neolithic asssemblage, we have so many small artefacts; so, I do not consider it),
# - feature frequency (we have some stone alignments, but we do not know the exact level, we know the area of those features),
# - retouch frequency: retouch_frequency
# - tool diversity (diversity of tool types within each assemblage, calculated using Menhinick’s index) BM: tool diversity from B & C: "calculated using the Menhinick’s index in which the number of tool types represented is divided by the square root of the total number of retouched tool".
sum_depth_sheet_for_pca <-
sum_depth_sheet %>%
mutate(
core_frequency = core_count / total_lithics,
blank_frequency = (flake_count + blade_count + bladelet_count) / total_lithics,
total_tools = retouched_tool_count + utilized_tool_count + shine_tool_count,
# Calculate tool diversity using Menhinick's index
tool_diversity = tool_type_count / sqrt(total_tools)) %>%
# drop rows that have no tools
filter(total_tools != 0)
# performing PCA
library(FactoMineR)
library(factoextra)
sum_depth_sheet_subset <-
sum_depth_sheet_for_pca %>%
drop_na(tool_diversity) %>%
# explore the effect of outliers on the PCA space
filter(!label2 %in% c("tp1_b_1_120_140",
"tp1_c_3_0_10"))
pca_data <-
sum_depth_sheet_subset %>%
select(lithic_density,
core_frequency,
blank_frequency,
retouch_frequency,
tool_diversity)
# Perform PCA
res.pca <- PCA(pca_data, graph = FALSE)
# View the summary results
# summary(res.pca)# PCA test
# BM: new method to me! I found https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8858582/
library(PCAtest)
# compute the tests and save the plot
jpeg( filename = here::here("figures/fig-pca-tests.jpg"),
height = 6,
width = 8,
units = "in",
res = 900)
result <-
PCAtest(pca_data,
1000,
1000,
0.05,
varcorr=FALSE,
counter=FALSE,
plot=TRUE)
Sampling bootstrap replicates... Please wait
Calculating confidence intervals of empirical statistics... Please wait
Sampling random permutations... Please wait
Comparing empirical statistics with their null distributions... Please wait
========================================================
Test of PCA significance: 5 variables, 29 observations
1000 bootstrap replicates, 1000 random permutations
========================================================
Empirical Psi = 3.4115, Max null Psi = 2.1034, Min null Psi = 0.1006, p-value = 0
Empirical Phi = 0.4130, Max null Phi = 0.3243, Min null Phi = 0.0709, p-value = 0
Empirical eigenvalue #1 = 2.45885, Max null eigenvalue = 2.18134, p-value = 0
Empirical eigenvalue #2 = 1.24267, Max null eigenvalue = 1.51665, p-value = 0.37
Empirical eigenvalue #3 = 0.82347, Max null eigenvalue = 1.19173, p-value = 0.961
Empirical eigenvalue #4 = 0.36085, Max null eigenvalue = 0.99001, p-value = 1
Empirical eigenvalue #5 = 0.11417, Max null eigenvalue = 0.80209, p-value = 1
PC 1 is significant and accounts for 49.2% (95%-CI:37.9-58.8) of the total variation
Variables 2, 3, and 4 have significant loadings on PC 1dev.off()quartz_off_screen
2 knitr::include_graphics(here::here("figures/fig-pca-tests.jpg"))
# Plot: Contribution of variables for each of the four relevant PCA dimensions
# save contribution plots into one objects
contribution_plots <-
map(1:4, ~fviz_contrib(res.pca,
choice = "var",
axes = .x,
top = 10))
#combine individual plots into one plot
library(cowplot)
plot_grid(plotlist = contribution_plots,
ncol = 2)
# BM: save this figure to paste into the
# drafting document to prepare for submission
ggsave(here::here("figures/fig-contribution-plots.jpg"),
h = 6,
w = 8)# SS: get the contributions of each variable to the first two principal components, which we can then use in the text.
res.pca <- PCA(pca_data)
# Contributions of variables to dimension 1 and 2:
contrib_dim1 <- res.pca$var$contrib[, 1]
contrib_dim2 <- res.pca$var$contrib[, 2]
contrib_dim3 <- res.pca$var$contrib[, 3]
contrib_dim4 <- res.pca$var$contrib[, 4]
contrib_dim5 <- res.pca$var$contrib[, 5]
# To view the contributions:
contrib_dim1 lithic_density core_frequency blank_frequency retouch_frequency
2.1779587 33.7190873 34.4425704 28.6953325
tool_diversity
0.9650512 contrib_dim2 lithic_density core_frequency blank_frequency retouch_frequency
50.789820 1.362289 5.432509 0.445294
tool_diversity
41.970087 contrib_dim3 lithic_density core_frequency blank_frequency retouch_frequency
32.374220 2.963017 1.609141 9.204529
tool_diversity
53.849093 contrib_dim4 lithic_density core_frequency blank_frequency retouch_frequency
12.961547 23.851227 2.247312 57.849983
tool_diversity
3.089930 contrib_dim5 lithic_density core_frequency blank_frequency retouch_frequency
1.6964535 38.1043792 56.2684675 3.8048612
tool_diversity
0.1258385 # screeplot; inspect distribution of PCs
fviz_screeplot(res.pca)
# Inspect eigenvalues
eigen_df <- tibble(
Eigenvalue = res.pca$eig[,1],
`Percentage of Variance` = res.pca$eig[,2],
`Cumulative Percentage of Variance` = res.pca$eig[,3]
)
library(kableExtra)
# Create a new column named "Dimension"
eigen_df$Dimension <-
paste("Dim", seq_len(nrow(eigen_df)), sep = "")
# Re-order the columns based on the corrected names
eigen_df <- eigen_df[, c("Dimension",
"Eigenvalue",
"Percentage of Variance",
"Cumulative Percentage of Variance")]
# Round the numerical columns to 3 decimal places
eigen_df[, 2:4] <- round(eigen_df[, 2:4], 2)
# BM: export this table as a CSV to paste into the
# drafting document to prepare for submission
write_csv(eigen_df,
here::here("data/derived-data/tbl-003-pca-eigenvalues.csv"))
# Creating the kable output
kable_output <- kable(eigen_df,
col.names = c("Dimension",
"Eigenvalue",
"Variance Percent",
"Cumulative Variance Percent"),
caption = "Eigenvalues and percentage of variance for each dimension of PCA")
# Display the table
kable_output | Dimension | Eigenvalue | Variance Percent | Cumulative Variance Percent |
|---|---|---|---|
| Dim1 | 2.46 | 49.18 | 49.18 |
| Dim2 | 1.24 | 24.85 | 74.03 |
| Dim3 | 0.82 | 16.47 | 90.50 |
| Dim4 | 0.36 | 7.22 | 97.72 |
| Dim5 | 0.11 | 2.28 | 100.00 |
library(ggrepel)
rownames(res.pca$ind$coord) <-
sum_depth_sheet_subset$label2
# get excavation area so we can use it for grouping
excavation_area <-
str_extract(sum_depth_sheet_subset$label2,
"[^_]+")
pca_data.pca <- prcomp(pca_data, scale. = TRUE)
library(ggpubr)
library(ggbiplot)
pca_data.pca <- prcomp(pca_data, scale. = TRUE)
biplot_modified <-
ggbiplot(
pca_data.pca,
obs.scale = 1,
var.scale = 1,
groups = excavation_area,
ellipse = FALSE,
) +
stat_chull(aes(color = excavation_area,
fill = excavation_area),
alpha = 0.1,
geom = "polygon") +
scale_colour_brewer(palette = "Set1",
name = '',
guide = 'none') +
scale_fill_brewer(palette = "Set1",
name = '') +
theme_minimal()
# Display the plot
biplot_modified
# BM: save this figure to paste into the
# drafting document to prepare for submission
ggsave(plot = biplot_modified,
filename = here::here("figures/fig-pca-biplot.jpg"),
h = 6,
w = 8)# PerMANOVA - partitioning the euclidean distance matrix by species
# from https://stackoverflow.com/a/20267537/1036500
library(vegan)
pca_data_for_post_hoc_testing <-
pca_data %>%
add_column(excavation_area)
# Is there are significant difference in the groups that
# we see in the PCA?
PerMANOVA_results <-
adonis2(pca_data[, 1:5] ~ excavation_area,
data = pca_data_for_post_hoc_testing,
method='eu')
PerMANOVA_results_inline <-
paste0("_F_(",
PerMANOVA_results$Df[1],
", ",
PerMANOVA_results$Df[2],
") = ",
round(PerMANOVA_results$F[1], 3),
" _p_ = ",
PerMANOVA_results$`Pr(>F)`[1]
)
# Which specific pairs of groups differ from each other?
# https://github.com/pmartinezarbizu/pairwiseAdonis
library(pairwiseAdonis)
pairwise.adonis2_results <-
pairwise.adonis2(pca_data[, 1:5] ~ excavation_area,
data = pca_data_for_post_hoc_testing)
# turn this output into a nice table
pairwise.adonis2_results_tbl <-
tibble(
# names
Pair = c(names(pairwise.adonis2_results[2]),
names(pairwise.adonis2_results[3]),
names(pairwise.adonis2_results[4])),
# F stat
F = c(pairwise.adonis2_results[2][[1]]$F[1],
pairwise.adonis2_results[3][[1]]$F[1],
pairwise.adonis2_results[4][[1]]$F[1]),
# p-values
p = c(pairwise.adonis2_results[2][[1]]$`Pr(>F)`[1],
pairwise.adonis2_results[3][[1]]$`Pr(>F)`[1],
pairwise.adonis2_results[4][[1]]$`Pr(>F)`[1])
) %>%
mutate(Pair = str_replace_all(Pair, "_", " "))
knitr::kable(pairwise.adonis2_results_tbl,
caption = "Summary of pairwise post-hoc tests on the excavation areas")Table 1: ?(caption)
| Pair | F | p |
|---|---|---|
| d1 vs ta | 1.031771 | 0.339 |
| d1 vs tp1 | 2.602013 | 0.070 |
| ta vs tp1 | 3.461623 | 0.052 |
A permutation MANOVA indicates that there is a significant difference in the lithic assemblage composition across the three excavation areas (F(2, 26) = 4.001 p = 0.031). We investigated this further using pairwise post-hoc tests and found that this significant difference is between TA and TP1, with the other two areas being statisically indistinguishable (Table 1 )